The underlying histopathology is very important in determining patient management, as the histopathology usually has direct repercussions on the treatment response and clinical course. However, the impact of the method used to assess renal biopsies, i.e., light microscopy (LM), immunofluorescence (IF), and electron microscopy (EM), on the occurrence of a difficult biopsy classification in the native kidneys of pediatric nephrotic patients is unknown. A 12-month-old Japanese boy was diagnosed with nephrotic syndrome (NS); he was administered prednisolone (60 mg/m(2)/day), and a continuous albumin infusion was started. A renal biopsy using LM revealed minimal change. However, an IF study showed granular staining for immunoglobulin G along the glomerular basement membrane. Therefore, he was diagnosed with membranous nephropathy (MN). As his proteinuria was so severe, we started immunosuppressant therapy and continued the albumin infusion for more than 2 months. However, he did not attain complete remission. A month later, EM examination of his renal biopsy showed extensive foot process fusion without electron-dense deposits. Although the result of the IF study suggested MN, the results of the LM and EM studies indicated minimal change. We finally diagnosed the patient with minimal change NS, in consideration of his clinical condition and course. Because of the failure of previous treatments, pulse steroid therapy was started. After five rounds of therapy the patient attained complete remission. A difficult renal biopsy finding classification, dependent on the diagnostic method used, might occur in the native kidneys of pediatric nephrotic patients. Therefore, a diagnosis should be made after considering all renal biopsy findings and the clinical course.